I think that after ASM3 will come Sinister Six and Venom. They want to create a shared Spider-Man universe so I think the Clone Saga would be the next logical step.
How they could pull this off?
Have the following characters actually be clones of Peter Parker:

Ben Riley: a straight up clone of Peter, dyes his hair blonde at the end and goes off in the Scarlet Spider costume as a new hero.
Miles Morales: a mix of Peter and Aaron Davis (the Prowler)'s DNA.
Jessica Drew: use the story like in the Ultimate Comics where she is Arachne, Clone of Peter.

You can also have Tarantula and Scorpion be minor villains as they were clones of Peter in the Ultimate comics.